Wiki

Function

Find programs by EDAM topic

Description

wosstopic searches the annotation of applications in ACD files, using terms from the EDAM ontology. There are various options for controlling how the search is performed and what is given in the output file. Optionally, the output will be wrapped in HTML tags ready for inclusion in a Web page.

Algorithm

The first search is of the EDAM ontology topic namespace, using the
term names and their synonynms. All child terms are automatically
included in the set of matches inless the -nosubclasses
qualifier is used.

The -sensitive qualifier also searches the definition strings.

The set of EDAM terms are then compared to relations in the ACD file,
where the application definition requires EDAM topic annotation.

Command line arguments

Find programs by EDAM topic
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-identifier] string Identifier(s) to search for in ontology (Any
string)
Additional (Optional) qualifiers:
-explode boolean [N] The groups that EMBOSS applications
belong to have two forms, exploded and not
exploded. The exploded group names are more
numerous and often vaguely phrased than the
non-exploded ones. The exploded names are
formed from definitions of the group names
that start like NAME1:NAME2 and which are
then expanded into many combinations of the
names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
NAME2 NAME1'. The non-expanded names are
simply like: 'NAME1 NAME2'.
-showkeywords boolean [N] Show keywords with program documentation
-outfile outfile [stdout] Tool metadata output file
-html toggle [N] If you are sending the output to a file,
this will format it for displaying as a
table in a WWW document.
-groups boolean [N] If you use this option, then only the
group names will be output to the file
-alphabetic boolean [N] If you use this option, then you will
get a single list of the program names and
descriptions instead of the programs being
listed in their functional groups.
Advanced (Unprompted) qualifiers:
-sensitive boolean [N] By default, the query keywords are
matched against the EDAM term names (and
synonyms) only. This option also matches the
keywords against the EDAM term definitions
and will therefore (typically) report more
matches.
-[no]subclasses boolean [Y] Extend the query matches to include all
terms which are specialisations (EDAM
sub-classes) of the matched type.
-obsolete boolean [N] The default behaviour is to not use or
return obsolete terms. This option if set
will include all terms.
-[no]emboss boolean [Y] If you use this option then EMBOSS
program documentation will be searched. If
this option is set to be false, then only
the EMBASSY programs will be searched (if
the -embassy option is true). EMBASSY
programs are not strictly part of EMBOSS,
but use the same code libraries and share
the same look and feel, but are generally
developed by people who wish the programs to
be outside of the GNU Public Licence scheme
-[no]embassy boolean [Y] If you use this option then EMBASSY
program documentation will be searched. If
this option is set to be false, then only
the EMBOSS programs will be searched (if the
-emboss option is true). EMBASSY programs
are not strictly part of EMBOSS, but use the
same code libraries and share the same look
and feel, but are generally developed by
people who wish the programs to be outside
of the GNU Public Licence scheme
-showembassy string If you use this option then this EMBASSY
package program documentation will be
searched. EMBASSY programs are not strictly
part of EMBOSS, but use the same code
libraries and share the same look and feel,
but are generally developed by people who
wish the programs to be outside of the GNU
Public Licence scheme (Any string)
-colon boolean [N] The groups that EMBOSS applications
belong to up to two levels, for example the
primary group 'ALIGNMENT' has several
sub-groups, or second-level groups, e.g.:
CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
LOCAL, MULTIPLE. To aid programs that parse
the output of wossname that require the
names of these subgroups, a colon ':' will
be placed between the first and second level
of the group name if this option is true.
Note: This does not apply if the group names
have been exploded with the 'explode'
option.
-gui boolean [N] This option is intended to help those
who are designing Graphical User Interfaces
to the EMBOSS applications. Some EMBOSS
programs are inappropriate for running in a
GUI, these include other menu programs and
interactive editors. This option allows you
to only report those programs that can be
run from a GUI
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-identifier](Parameter 1)

string

Identifier(s) to search for in ontology

Any string

Additional (Optional) qualifiers

-explode

boolean

The groups that EMBOSS applications belong to have two forms, exploded and not exploded. The exploded group names are more numerous and often vaguely phrased than the non-exploded ones. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: 'NAME1', 'NAME2', 'NAME1 NAME2', NAME2 NAME1'. The non-expanded names are simply like: 'NAME1 NAME2'.

Boolean value Yes/No

No

-showkeywords

boolean

Show keywords with program documentation

Boolean value Yes/No

No

-outfile

outfile

Tool metadata output file

Output file

stdout

-html

toggle

If you are sending the output to a file, this will format it for displaying as a table in a WWW document.

Toggle value Yes/No

No

-groups

boolean

If you use this option, then only the group names will be output to the file

Boolean value Yes/No

No

-alphabetic

boolean

If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups.

Boolean value Yes/No

No

Advanced (Unprompted) qualifiers

-sensitive

boolean

By default, the query keywords are matched against the EDAM term names (and synonyms) only. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches.

Boolean value Yes/No

No

-[no]subclasses

boolean

Extend the query matches to include all terms which are specialisations (EDAM sub-classes) of the matched type.

Boolean value Yes/No

Yes

-obsolete

boolean

The default behaviour is to not use or return obsolete terms. This option if set will include all terms.

Boolean value Yes/No

No

-[no]emboss

boolean

If you use this option then EMBOSS program documentation will be searched. If this option is set to be false, then only the EMBASSY programs will be searched (if the -embassy option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme

Boolean value Yes/No

Yes

-[no]embassy

boolean

If you use this option then EMBASSY program documentation will be searched. If this option is set to be false, then only the EMBOSS programs will be searched (if the -emboss option is true). EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme

Boolean value Yes/No

Yes

-showembassy

string

If you use this option then this EMBASSY package program documentation will be searched. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme

Any string

-colon

boolean

The groups that EMBOSS applications belong to up to two levels, for example the primary group 'ALIGNMENT' has several sub-groups, or second-level groups, e.g.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE. To aid programs that parse the output of wossname that require the names of these subgroups, a colon ':' will be placed between the first and second level of the group name if this option is true. Note: This does not apply if the group names have been exploded with the 'explode' option.

Boolean value Yes/No

No

-gui

boolean

This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors. This option allows you to only report those programs that can be run from a GUI

Boolean value Yes/No

No

Associated qualifiers

"-outfile" associated outfile qualifiers

-odirectory

string

Output directory

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

N

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

N

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

N

-warning

boolean

Report warnings

Boolean value Yes/No

Y

-error

boolean

Report errors

Boolean value Yes/No

Y

-fatal

boolean

Report fatal errors

Boolean value Yes/No

Y

-die

boolean

Report dying program messages

Boolean value Yes/No

Y

-version

boolean

Report version number and exit

Boolean value Yes/No

N

Input file format

wosstopic reads the brief descriptions and the program groups from
the ACD files. (ACD files control the parameters that the programs
expect - don't worry about them unless you are writing EMBOSS
programs).

Output file format

The results are written out as a simple list of program names and
short descriptions.